Are you saying you want 3 total switches (master on/off, on/off for each separate effect) and a toggle for the effect order?
In that case the in/out jacks would go to the master on/off switch, which would then connect to the order switching board. The individual in/out of each effect PCB would also go to the order switching board.
The master on/off LED would just need a few legs of the 3pdt switch with one leg of the LED connecting to 9v and the other through a resistor to a lug on the switch (other lug to ground).